rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
172,DRR075398,DRX069312,DRS075493,DRP004473,PRJDB5226,Effects of local gut tumor on whole organismal gene expressions in zebrafish,DRP004473,Other,How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.,,,The gut of control fish 7dpf,Control gut,SAMD00065412,,sample name:2 control gut 150701 Hiseq3A l3 018|tissue type:Gut,,,,,,,,,Illumina HiSeq 2500 sequencing of SAMD00065412,DRX069312,Control gut,1,Agilent SureSelect Strand Specific RNA Prep Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,360Application ReadForward1,DRP004473,Illumina HiSeq 2500 sequencing of SAMD00065412,,,,1008093492.0,28002597.0,DRR075398,0:36,A:230431417;C:251640901;G:244174255;T:281811580;N:35339,36,,,,230431417,251640901,244174255,281811580,35339,DRX069312,DRS075493,DRA005199,"ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International","The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International",1,0.9173,,0.07181,,0.72017,,0.45193,,36,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2018-09-19,Larval,Larval,Gut,Digestive System
9166,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female 1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,8660FApplication ReadForward11RApplication ReadReverse434,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,8660FApplication ReadForward11RApplication ReadReverse434,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,8660FApplication ReadForward11RApplication ReadReverse434,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min 65°C for 30 min held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,8660FApplication ReadForward11RApplication ReadReverse434,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
29041,SRR26990794,SRX22683825,SRS19677539,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut3,GSM7924158,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924158,GSM7924158: WT gut3; Danio rerio; RNA Seq,GSM7924158 r1,GSM7924158,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,12_WT_3G_S27_L001_R2_001.fastq.gz 12_WT_3G_S27_L001_R1_001.fastq.gz,fastq fastq,6066709786.0,20088443.0,GSM7924158 r1,0:151 1:151,A:1673762656;C:1360901090;G:1385125931;T:1646863953;N:56156,151,151,,,1673762656,1360901090,1385125931,1646863953,56156,SRX22683825,SRS19677539,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.92515,0.9297,0.0691,0.0659,0.75041,0.75022,0.53007,0.53064,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29042,SRR26990795,SRX22683824,SRS19677538,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut2,GSM7924157,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924157,GSM7924157: WT gut2; Danio rerio; RNA Seq,GSM7924157 r1,GSM7924157,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,11_WT_2G_S26_L001_R2_001.fastq.gz 11_WT_2G_S26_L001_R1_001.fastq.gz,fastq fastq,5406867570.0,17903535.0,GSM7924157 r1,0:151 1:151,A:1464846243;C:1237183908;G:1259215309;T:1445572498;N:49612,151,151,,,1464846243,1237183908,1259215309,1445572498,49612,SRX22683824,SRS19677538,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93795,0.94322,0.05952,0.05592,0.75933,0.75887,0.54179,0.53451,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29043,SRR26990796,SRX22683823,SRS19677537,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,WT gut1,GSM7924156,,source name:gut|tissue:gut|genotype:wildtype|time:50dpf|geo loc name:missing|collection date:missing,WT gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:wildtype|time:50dpf,GSM7924156,GSM7924156: WT gut1; Danio rerio; RNA Seq,GSM7924156 r1,GSM7924156,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,10_WT_1G_S25_L001_R1_001.fastq.gz 10_WT_1G_S25_L001_R2_001.fastq.gz,fastq fastq,5162192908.0,17093354.0,GSM7924156 r1,0:151 1:151,A:1404682153;C:1175657030;G:1196829496;T:1384975886;N:48343,151,151,,,1404682153,1175657030,1196829496,1384975886,48343,SRX22683823,SRS19677537,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93119,0.93585,0.06122,0.05809,0.74757,0.74757,0.54124,0.54417,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29044,SRR26990797,SRX22683822,SRS19677536,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut3,GSM7924155,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut3,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924155,GSM7924155: itgavKO gut3; Danio rerio; RNA Seq,GSM7924155 r1,GSM7924155,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,9_itgavKO_3G_S24_L001_R2_001.fastq.gz 9_itgavKO_3G_S24_L001_R1_001.fastq.gz,fastq fastq,4146743578.0,13730939.0,GSM7924155 r1,0:151 1:151,A:1130002132;C:943522869;G:958031732;T:1115146458;N:40387,151,151,,,1130002132,943522869,958031732,1115146458,40387,SRX22683822,SRS19677536,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.93764,0.94144,0.05938,0.05594,0.7553,0.75485,0.55535,0.55018,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29045,SRR26990798,SRX22683821,SRS19677535,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itgavKO gut2,GSM7924154,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itgavKO gut2,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924154,GSM7924154: itgavKO gut2; Danio rerio; RNA Seq,GSM7924154 r1,GSM7924154,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,8_itgavKO_2G_S23_L001_R1_001.fastq.gz 8_itgavKO_2G_S23_L001_R2_001.fastq.gz,fastq fastq,4225756140.0,13992570.0,GSM7924154 r1,0:151 1:151,A:1133211420;C:974497998;G:995876972;T:1122129220;N:40530,151,151,,,1133211420,974497998,995876972,1122129220,40530,SRX22683821,SRS19677535,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.95341,0.95884,0.05109,0.04883,0.77542,0.77368,0.51301,0.50704,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
29046,SRR26990799,SRX22683820,SRS19677534,SRP474986,PRJNA1046526,ITGAV variants are associated with immune dysregulation brain abnormalities and very early onset Inflammatory Bowel Disease,GSE248975,Transcriptome Analysis,Integrin alpha–V ITGAV forms heterodimers with beta subunits to regulate several cellular processes including transforming growth factor ß TGF ß signaling. We examined three unrelated families with common disease features including two children born with congenital brain anomalies and later development of immune dysregulation atopy and colitis and three fetuses with brain and developmental defects. Using whole exome and RNA sequencing and functional studies we demonstrate that biallelic ITGAV variants caused abnormal splicing or mislocalized protein that led to dysregulated TGF ß signaling in these families. Furthermore knockout itgav / zebrafish embryos developed brain defects with loss of microglia and juvenile itgav / zebrafish developed colitis. Together we show the critical role of ITGAV in immune regulation and gut and brain homeostasis and disease pathogenesis. Overall design: To investigate the role of itgav in the development of very early onset inflammatory bowel disease we generated zebrafish itgav knock out line using CRISPR/Cas9 technology. We then perform gene expression profile analysis using data abtained from RNAseq from wild type zebrafish line and itgav / line at two timepoints 8 dpf and 50 dpf. Comparative gene expression profiling analysis between wt and itgavKO zebrafish mutant were performed to examine the transcriptomic alterations caused by itgav deficiency.,,pubmed:39526957,,itagvKO gut1,GSM7924153,,source name:gut|tissue:gut|genotype:itgavKO mutant|time:50dpf|geo loc name:missing|collection date:missing,itagvKO gut1,The raw RNAseq reads were aligned to the zebrafish genome GRCz11 using hisat2. Reads in genes were counted using featureCounts. Differential gene expression was performed in R with the DESeq2 Assembly: zebrafish GRCz11 Supplementary files format and content: tab delimited text files include the count values for each Sample. Rows = genes; Columns = samples.,gut,Wt and itgav KO mutants at 8dpf underwent tailfin clipping genotyping.The wildtype and itgav / mutants were pooled n=15 repectively. Wt and itgav KO mutants at 50dpf underwent tailfin clipping genotyping. The wt and itgav KO mutant were euthanized by a overdose of tricaine and subsequently dissected. The gut brain and heart tissues were collected for RNA extration.,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,For wt and itgav KO mutants at 8dpf embryos were obtained via natural mating and cultured in embryo E3 buffer raised in 10cm petridish with E2 embryonic buffer and incubated at 28.5°C. For wt and itgav KO mutants at 50dpf embryos were kept in a circulating system that continuously filters and aerates the system water to maintain the water quality required for a healthy aquatic environment. Temperature ranges from 26 28.5°C and the lighting conditions are 14:10 hr light: dark.,tissue:gut|genotype:itgavKO mutant|time:50dpf,GSM7924153,GSM7924153: itagvKO gut1; Danio rerio; RNA Seq,GSM7924153 r1,GSM7924153,1,RNA were extracted using RNAeasy mini kitQiagen. 600ng of total RNA were used for the construction of sequencing libraries. RNA library preparation follows the Illumina® Stranded Total RNA Prep with Ribo Zero Plus protocol to generate polyA enriched rRNA depleted libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP474986,,loader:fastq load.py,7_itagvKO_1G_S22_L001_R1_001.fastq.gz 7_itagvKO_1G_S22_L001_R2_001.fastq.gz,fastq fastq,5954117844.0,19715622.0,GSM7924153 r1,0:151 1:151,A:1600496071;C:1372939932;G:1393534700;T:1587094282;N:52859,151,151,,,1600496071,1372939932,1393534700,1587094282,52859,SRX22683820,SRS19677534,SRA1760061,"Muise Lab, Cell Biology, The Hospital for Sick Children","Muise Lab, Cell Biology, The Hospital for Sick Children",2,0.94807,0.95298,0.05682,0.05385,0.74004,0.73925,0.54423,0.54484,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,ribozero,bulk,unknown,unknown,,Canada,2023-11-29,Multi-stage,Multi-stage,Gut,Digestive System
30620,SRR27907608,SRX23567386,SRS20412878,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO12. Ctla 4 knockout,GSM8068839,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO12. Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068839,GSM8068839: KO12. Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068839 r1,GSM8068839,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO12_Clean_Data2.fq.gz KO12_Clean_Data1.fq.gz,fastq fastq,5415971621.0,18199812.0,GSM8068839 r1,0:148.79 1:148.79,A:1482389043;C:1213758088;G:1232295642;T:1487496355;N:32493,148,148,,,1482389043,1213758088,1232295642,1487496355,32493,SRX23567386,SRS20412878,SRA1799527,zhejiang university,zhejiang university,2,0.86496,0.86584,0.08493,0.08156,0.73553,0.73588,0.50941,0.5104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30621,SRR27907609,SRX23567385,SRS20412877,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO11 Ctla 4 knockout,GSM8068838,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO11 Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068838,GSM8068838: KO11 Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068838 r1,GSM8068838,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO11_Clean_Data2.fq.gz KO11_Clean_Data1.fq.gz,fastq fastq,5443694370.0,18290488.0,GSM8068838 r1,0:148.81 1:148.81,A:1480267395;C:1230300897;G:1247791644;T:1485302181;N:32253,148,148,,,1480267395,1230300897,1247791644,1485302181,32253,SRX23567385,SRS20412877,SRA1799527,zhejiang university,zhejiang university,2,0.86445,0.86409,0.07094,0.06652,0.74738,0.74897,0.51339,0.51762,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30622,SRR27907610,SRX23567384,SRS20412876,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,KO9 Ctla 4 knockout,GSM8068837,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO9 Ctla 4 knockout,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068837,GSM8068837: KO9 Ctla 4 knockout; Danio rerio; RNA Seq,GSM8068837 r1,GSM8068837,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,KO9_Clean_Data2.fq.gz KO9_Clean_Data1.fq.gz,fastq fastq,5971590749.0,20072217.0,GSM8068837 r1,0:148.76 1:148.75,A:1640322573;C:1334570646;G:1352953128;T:1643708463;N:35939,148,148,,,1640322573,1334570646,1352953128,1643708463,35939,SRX23567384,SRS20412876,SRA1799527,zhejiang university,zhejiang university,2,0.86793,0.86937,0.07855,0.07588,0.74393,0.74523,0.50694,0.51104,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30623,SRR27907611,SRX23567383,SRS20412875,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT8 control,GSM8068836,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT8 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068836,GSM8068836: WT8 control; Danio rerio; RNA Seq,GSM8068836 r1,GSM8068836,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT8_Clean_Data1.fq.gz WT8_Clean_Data2.fq.gz,fastq fastq,5740688401.0,19287992.0,GSM8068836 r1,0:148.82 1:148.81,A:1586419463;C:1274440057;G:1291660517;T:1588132746;N:35618,148,148,,,1586419463,1274440057,1291660517,1588132746,35618,SRX23567383,SRS20412875,SRA1799527,zhejiang university,zhejiang university,2,0.85516,0.85653,0.07987,0.07551,0.74515,0.74497,0.52575,0.52057,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30624,SRR27907612,SRX23567382,SRS20412874,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT7 control,GSM8068835,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT7 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068835,GSM8068835: WT7 control; Danio rerio; RNA Seq,GSM8068835 r1,GSM8068835,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT7_Clean_Data2.fq.gz WT7_Clean_Data1.fq.gz,fastq fastq,5810188177.0,19521216.0,GSM8068835 r1,0:148.82 1:148.81,A:1609284873;C:1285068093;G:1302652710;T:1613147856;N:34645,148,148,,,1609284873,1285068093,1302652710,1613147856,34645,SRX23567382,SRS20412874,SRA1799527,zhejiang university,zhejiang university,2,0.83558,0.83684,0.08427,0.08011,0.75741,0.75836,0.52403,0.52405,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30625,SRR27907613,SRX23567381,SRS20412873,SRP488782,PRJNA1074407,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [bulkRNA seq],GSE255304,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,pubmed:40392591,,WT1 control,GSM8068834,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT1 control,The differentially expressed genes DEGs were identified with absolute Log2 fold change > 1 and adjusted p value < 0.05 by R package DESeq2. Gene Ontology GO enrichment and Kyoto encyclopedia of genes and genomes KEGG enrichment analyses were performed by the OmicStudio http://www.omicstudio.cn/tool tools. Gene set enrichment analysis was performed using software GSEA v4.1.0 https://www.gsea msigdb.org/gsea/index.jsp and the heatmap was generated using the R package ggplot2. For the protein protein interaction PPI networks the DEGs were retrieved in STRING version 11.5 https://string db.org/ database combined score > 0.4 and the PPI network was visualized by Cytoscape software version 3.9.16. The betweenness centrality BC was calculated using the CytoNCA plugin in Cytoscape software. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068834,GSM8068834: WT1 control; Danio rerio; RNA Seq,GSM8068834 r1,GSM8068834,1,Total RNAs were isolated from wild type or ctla 4 / intestines three biological replicates using TRIzol reagent following the manufacturer's instructions Takara. cDNA libraries were constructed using NEB Next Ultra Directional RNA Library Prep Kit NEB and sequencing was performed according to the Illumina Hiseq2500 standard protocol at LC Bio Hangzhou China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP488782,,loader:fastq load.py,WT1_Clean_Data2.fq.gz WT1_Clean_Data1.fq.gz,fastq fastq,5771161671.0,19396834.0,GSM8068834 r1,0:148.77 1:148.76,A:1593780869;C:1284499295;G:1300298518;T:1592548515;N:34474,148,148,,,1593780869,1284499295,1300298518,1592548515,34474,SRX23567381,SRS20412873,SRA1799527,zhejiang university,zhejiang university,2,0.85731,0.85944,0.0704,0.06703,0.76601,0.76607,0.53065,0.53445,149,149,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30626,SRR27907720,SRX23567476,SRS20412967,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,KO scRNAseq,GSM8068833,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO scRNAseq,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068833,GSM8068833: KO scRNAseq; Danio rerio; RNA Seq,GSM8068833 r1,GSM8068833,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz,fastq fastq,40958285011.0,344187269.0,GSM8068833 r1,0:28 1:91,A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185,28,91,,,11614416767,9247684357,9480911439,10614469263,803185,SRX23567476,SRS20412967,SRA1799569,zhejiang university,zhejiang university,2,0.00982,0.9431,0.00356,0.10625,0.99277,0.8187,0.41297,0.63838,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30627,SRR27907721,SRX23567475,SRS20412966,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood but genetic factors have implicated in genome wide association studies including CTLA 4 an essential negative regulator of T cell activation. However establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 / zebrafish line. These mutant zebrafish exhibit reduced weight along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes disturbing immune system homeostasis. Moreover single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,WT scRNAseq,GSM8068832,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT scRNAseq,The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068832,GSM8068832: WT scRNAseq; Danio rerio; RNA Seq,GSM8068832 r1,GSM8068832,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq,36724066995.0,308605605.0,GSM8068832 r1,0:28 1:91,A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801,28,91,,,10425178276,8399183780,8411777361,9487202777,724801,SRX23567475,SRS20412966,SRA1799569,zhejiang university,zhejiang university,2,0.01141,0.94944,0.0039,0.1092,0.99324,0.841,0.43558,0.73314,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30694,SRR28272066,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz,fastq fastq,6487168261.0,54514019.0,GSM8136771 r1,0:28 1:91,A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286,28,91,,,1754199332,1533792234,1687916105,1511168304,92286,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30695,SRR28272067,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775 HuNoV infected replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775 HuNoV infected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775 HuNoV infected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz,fastq fastq,6313572727.0,53055233.0,GSM8136771 r2,0:28 1:91,A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282,28,91,,,1709609257,1491468410,1640296277,1472111501,87282,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30696,SRR28272068,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz,fastq fastq,15738518978.0,132256462.0,GSM8136770 r1,0:28 1:91,A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212,28,91,,,4181691582,3761213961,4083789142,3711597081,227212,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30697,SRR28272069,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774 HuNoV infected replicate 1 scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774 HuNoV infected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774 HuNoV infected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz,fastq fastq,15261653253.0,128249187.0,GSM8136770 r2,0:28 1:91,A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693,28,91,,,4059552936,3644406570,3954261902,3603216152,215693,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30698,SRR28272070,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz,fastq fastq,15150656598.0,127316442.0,GSM8136769 r1,0:28 1:91,A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113,28,91,,,4100783574,3526779401,3845684506,3677189004,220113,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30699,SRR28272071,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773 uninfected replicate 2 scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773 uninfected replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773 uninfected replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz,fastq fastq,14942015326.0,125563154.0,GSM8136769 r2,0:28 1:91,A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808,28,91,,,4048600218,3475105088,3787275869,3630822343,211808,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30700,SRR28272072,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz,fastq fastq,7397061301.0,62160179.0,GSM8136768 r1,0:28 1:91,A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806,28,91,,,2023651844,1711760729,1860691426,1800850496,106806,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30701,SRR28272073,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease yet critical aspects of their biology including cellular tropism remain unclear. While research traditionally focused on the intestinal epithelium the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication as all three open reading frames were mapped to individual macrophages. Yet macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772 uninfected replicate 1 scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772 uninfected replicate 1 scRNAseq,Cell Ranger v3.0 10X Genomics Pleasanton California USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772 uninfected replicate 1 scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase 40 µg/mL proteinase K 0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz,fastq fastq,7290496444.0,61264676.0,GSM8136768 r2,0:28 1:91,A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196,28,91,,,1996736343,1685693360,1830823892,1777138653,104196,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
33014,SRR29633212,SRX25139207,SRS21831220,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz 5dpf,GSM8366963,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366963,GSM8366963: Mtz 5dpf; Danio rerio; RNA Seq,GSM8366963 r1,GSM8366963,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz,fastq fastq,105173263361.0,348971465.0,GSM8366963 r1,0:150.76 1:150.62,A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203,150,150,,,29260313483,18342577741,20471735616,37097033318,1603203,SRX25139207,SRS21831220,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.56019,0.89517,0.13273,0.11945,0.9795,0.82258,0.63676,0.6161,151,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33015,SRR29633213,SRX25139206,SRS21831219,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control 5dpf,GSM8366962,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control 5dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366962,GSM8366962: Control 5dpf; Danio rerio; RNA Seq,GSM8366962 r1,GSM8366962,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz,fastq fastq,139967773505.0,464402100.0,GSM8366962 r1,0:150.76 1:150.63,A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516,150,150,,,39202616731,24289494719,27175225437,49298534102,1902516,SRX25139206,SRS21831219,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.54902,0.89315,0.13449,0.13341,0.97954,0.80553,0.69256,0.59244,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33016,SRR29633214,SRX25139205,SRS21831218,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Mtz ablation 4dpf,GSM8366961,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366961,GSM8366961: Mtz ablation 4dpf; Danio rerio; RNA Seq,GSM8366961 r1,GSM8366961,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz,Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,33049837760.0,103280743.0,GSM8366961 r1,0:150 1:150 2:10 3:10,A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545,150,150,10,10,9739096160,6338831532,6106096444,8799858219,340545,SRX25139205,SRS21831218,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.0,0.91169,0.0,0.19328,1.0,0.81722,,0.64993,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33017,SRR29633215,SRX25139204,SRS21831217,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation and DAPI live cells were sorted by FACS.,,pubmed:40252728,,Control ablation 4dpf,GSM8366960,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control ablation 4dpf,Demultiplexing of raw Illumina sequencing files barcoding processing gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366960,GSM8366960: Control ablation 4dpf; Danio rerio; RNA Seq,GSM8366960 r1,GSM8366960,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5% filtered with a 70µm membrane and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options: readTypes=BBTT read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz,Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz,fastq fastq fastq fastq,115286504000.0,360270325.0,GSM8366960 r1,0:150 1:150 2:10 3:10,A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542,150,150,10,10,32679027944,17748865933,17885040590,39764959491,3203542,SRX25139204,SRS21831217,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.39015,0.90036,0.10989,0.19421,0.97845,0.79401,0.69547,0.6103,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33351,SRR30125634,SRX25595192,SRS22245033,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 3,GSM8439539,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439539,GSM8439539: SBM1 3; Danio rerio; RNA Seq,GSM8439539 r1,GSM8439539,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-3.R1.fq.gz SBM1-3.R2.fq.gz,fastq fastq,6920938402.0,24030624.0,GSM8439539 r1,0:144.00 1:144.00,A:1848518187;C:1602695225;G:1609135376;T:1860572175;N:17439,144,144,,,1848518187,1602695225,1609135376,1860572175,17439,SRX25595192,SRS22245033,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33352,SRR30125635,SRX25595191,SRS22245032,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 2,GSM8439538,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439538,GSM8439538: SBM1 2; Danio rerio; RNA Seq,GSM8439538 r1,GSM8439538,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-2.R1.fq.gz SBM1-2.R2.fq.gz,fastq fastq,6873386097.0,23812133.0,GSM8439538 r1,0:144.32 1:144.33,A:1794801562;C:1631426136;G:1638460090;T:1808681001;N:17308,144,144,,,1794801562,1631426136,1638460090,1808681001,17308,SRX25595191,SRS22245032,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33353,SRR30125636,SRX25595190,SRS22245031,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,SBM1 1,GSM8439537,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,SBM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439537,GSM8439537: SBM1 1; Danio rerio; RNA Seq,GSM8439537 r1,GSM8439537,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,SBM1-1.R1.fq.gz SBM1-1.R2.fq.gz,fastq fastq,6893638362.0,23881631.0,GSM8439537 r1,0:144.33 1:144.33,A:1801507713;C:1634518350;G:1642455999;T:1815139080;N:17220,144,144,,,1801507713,1634518350,1642455999,1815139080,17220,SRX25595190,SRS22245031,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33354,SRR30125637,SRX25595189,SRS22245030,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 3,GSM8439536,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439536,GSM8439536: FM1 3; Danio rerio; RNA Seq,GSM8439536 r1,GSM8439536,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-3.R1.fq.gz FM1-3.R2.fq.gz,fastq fastq,6926890624.0,24044310.0,GSM8439536 r1,0:144.04 1:144.05,A:1814868011;C:1638590076;G:1645410775;T:1828004537;N:17225,144,144,,,1814868011,1638590076,1645410775,1828004537,17225,SRX25595189,SRS22245030,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33355,SRR30125638,SRX25595188,SRS22245029,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 2,GSM8439535,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439535,GSM8439535: FM1 2; Danio rerio; RNA Seq,GSM8439535 r1,GSM8439535,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-2.R1.fq.gz FM1-2.R2.fq.gz,fastq fastq,6932329149.0,24050700.0,GSM8439535 r1,0:144.12 1:144.12,A:1821635965;C:1634568957;G:1641356498;T:1834750114;N:17615,144,144,,,1821635965,1634568957,1641356498,1834750114,17615,SRX25595188,SRS22245029,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33356,SRR30125639,SRX25595187,SRS22245028,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,FM1 1,GSM8439534,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,FM1 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439534,GSM8439534: FM1 1; Danio rerio; RNA Seq,GSM8439534 r1,GSM8439534,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,FM1-1.R1.fq.gz FM1-1.R2.fq.gz,fastq fastq,6915521492.0,24044109.0,GSM8439534 r1,0:143.81 1:143.81,A:1851629842;C:1595942468;G:1602547587;T:1865384194;N:17401,143,143,,,1851629842,1595942468,1602547587,1865384194,17401,SRX25595187,SRS22245028,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33357,SRR30125640,SRX25595186,SRS22245027,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 3,GSM8439533,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 3,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439533,GSM8439533: D3 4 3; Danio rerio; RNA Seq,GSM8439533 r1,GSM8439533,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-3.R1.fq.gz D3-4-3.R2.fq.gz,fastq fastq,6934859246.0,24095045.0,GSM8439533 r1,0:143.91 1:143.91,A:1815846879;C:1641161510;G:1648091770;T:1829741658;N:17429,143,143,,,1815846879,1641161510,1648091770,1829741658,17429,SRX25595186,SRS22245027,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33358,SRR30125641,SRX25595185,SRS22245026,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 2,GSM8439532,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 2,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439532,GSM8439532: D3 4 2; Danio rerio; RNA Seq,GSM8439532 r1,GSM8439532,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-2.R1.fq.gz D3-4-2.R2.fq.gz,fastq fastq,7053487385.0,24519028.0,GSM8439532 r1,0:143.83 1:143.84,A:1888591272;C:1630003556;G:1636509489;T:1898365125;N:17943,143,143,,,1888591272,1630003556,1636509489,1898365125,17943,SRX25595185,SRS22245026,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33359,SRR30125642,SRX25595184,SRS22245025,SRP524094,PRJNA1144090,Beta Beta Dimethylacryloyl shikonin mechanism of preventing and treating zebrafish soybean meal enteritis,GSE273916,Transcriptome Analysis,The aim of this study is to explore through transcriptomics ß ß Dimethylacryloyl shikonin mechanism for preventing and treating in zebrafish. Overall design: We set up the FM group the SBM group andthe D3 group with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.,,,,D3 4 1,GSM8439531,,source name:intestine|tissue:intestine|geo loc name:missing|collection date:missing,D3 4 1,CLC Genomics Workbench v 11.0.1 Assembly: Danio rerio Supplementary files format and content: tab delimited text fles include FPKM values for each Sample,intestine,,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,tissue:intestine,GSM8439531,GSM8439531: D3 4 1; Danio rerio; RNA Seq,GSM8439531 r1,GSM8439531,1,RNA was harvested using Rneasy mini plus kitQiagen.1.3 ug of total RNA was used for the construction of sequencing libraries. RNA Ilbraries for RNA seq were prepared using SMAR TER mRNA Seq library Prep Kit following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524094,,,D3-4-1.R1.fq.gz D3-4-1.R2.fq.gz,fastq fastq,6996797279.0,24229469.0,GSM8439531 r1,0:144.38 1:144.39,A:1841905352;C:1647600285;G:1654313322;T:1852960597;N:17723,144,144,,,1841905352,1647600285,1654313322,1852960597,17723,SRX25595184,SRS22245025,SRA1939628,Beibu Gulf University,Beibu Gulf University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-08-04,Undetermined,Undetermined,Gut,Digestive System
33417,SRR30186672,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz,fastq fastq fastq,40502433410.0,130653011.0,GSM8448586 r1,0:8 1:151 2:151,A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043,8,151,151,,10014178947,5704376875,6596271508,17137143949,5238043,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33418,SRR30186673,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz,fastq fastq fastq,41972742020.0,135395942.0,GSM8448586 r2,0:8 1:151 2:151,A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929,8,151,151,,10346550415,6105559893,6757897068,17672755179,6811929,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33419,SRR30186674,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz,fastq fastq fastq,21590505830.0,69646793.0,GSM8448585 r1,0:8 1:151 2:151,A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913,8,151,151,,5324745627,3047288539,3517496789,9140955618,2844913,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33420,SRR30186675,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz,fastq fastq fastq,22493595040.0,72559984.0,GSM8448585 r2,0:8 1:151 2:151,A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039,8,151,151,,5532271824,3275587569,3623404196,9478183540,3668039,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33421,SRR30186676,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L005_I1_001.fastq.gz FT-SA26635_S3_L005_R1_001.fastq.gz FT-SA26635_S3_L005_R2_001.fastq.gz,fastq fastq fastq,29011782450.0,93586395.0,GSM8448584 r1,0:8 1:151 2:151,A:7041483148;C:4220842692;G:4903817651;T:12093250712;N:3697087,8,151,151,,7041483148,4220842692,4903817651,12093250712,3697087,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33422,SRR30186677,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L006_I1_001.fastq.gz FT-SA26635_S3_L006_R1_001.fastq.gz FT-SA26635_S3_L006_R2_001.fastq.gz,fastq fastq fastq,30061975960.0,96974116.0,GSM8448584 r2,0:8 1:151 2:151,A:7272472037;C:4518131790;G:5023942263;T:12466801069;N:4835873,8,151,151,,7272472037,4518131790,5023942263,12466801069,4835873,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33423,SRR30186678,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L005_I1_001.fastq.gz FT-SA26634_S2_L005_R1_001.fastq.gz FT-SA26634_S2_L005_R2_001.fastq.gz,fastq fastq fastq,28701845380.0,92586598.0,GSM8448583 r1,0:8 1:151 2:151,A:6898569356;C:4281479855;G:4993869601;T:11783488306;N:3745478,8,151,151,,6898569356,4281479855,4993869601,11783488306,3745478,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33424,SRR30186679,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L006_I1_001.fastq.gz FT-SA26634_S2_L006_R1_001.fastq.gz FT-SA26634_S2_L006_R2_001.fastq.gz,fastq fastq fastq,29814490250.0,96175775.0,GSM8448583 r2,0:8 1:151 2:151,A:7143218463;C:4592538828;G:5130593993;T:12173956857;N:4775909,8,151,151,,7143218463,4592538828,5130593993,12173956857,4775909,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33425,SRR30186680,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L005_I1_001.fastq.gz FT-SA26633_S1_L005_R1_001.fastq.gz FT-SA26633_S1_L005_R2_001.fastq.gz,fastq fastq fastq,16641390240.0,53681904.0,GSM8448582 r1,0:8 1:151 2:151,A:3957785280;C:2573469243;G:2993166279;T:6685407270;N:2106936,8,151,151,,3957785280,2573469243,2993166279,6685407270,2106936,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System
33426,SRR30186681,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally we show that functional perturbation of select transcription factors Ebf1a Gata3 and Satb2 alters the cell fate choice respectively of inhibitory excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2 3 4 5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222 followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20 23 28 32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system with pipetting up and down every 5 minutes. post digestion Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution no calcium no magnesium HBSS;10mM HEPES adjusted to PH 8.0; 2.5 mg/ml BSA and samples were then passed through a 70um cell strainer into 50ml conical tube centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L006_I1_001.fastq.gz FT-SA26633_S1_L006_R1_001.fastq.gz FT-SA26633_S1_L006_R2_001.fastq.gz,fastq fastq fastq,17304656010.0,55821471.0,GSM8448582 r2,0:8 1:151 2:151,A:4101777717;C:2763806899;G:3078134302;T:6911601509;N:2763815,8,151,151,,4101777717,2763806899,3078134302,6911601509,2763815,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System
34137,SRR31360761,SRX26734629,SRS23224778,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT3,,strain:AB|isolate:WT3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT3.fq,WT3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT3_R1.fq.gz WT3_R2.fq.gz,fastq fastq,7045875300.0,23486251.0,WT3 R1.fq.gz,0:150 1:150,A:1817741681;C:1708030651;G:1712073267;T:1808003621;N:26080,150,150,,,1817741681,1708030651,1712073267,1808003621,26080,SRX26734629,SRS23224778,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34138,SRR31360762,SRX26734628,SRS23224777,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT2,,strain:AB|isolate:WT2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT2.fq,WT2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT2_R1.fq.gz WT2_R2.fq.gz,fastq fastq,6888570900.0,22961903.0,WT2 R1.fq.gz,0:150 1:150,A:1774584110;C:1673773734;G:1678866397;T:1761321702;N:24957,150,150,,,1774584110,1673773734,1678866397,1761321702,24957,SRX26734628,SRS23224777,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34139,SRR31360763,SRX26734627,SRS23224776,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,WT1,,strain:AB|isolate:WT1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,WT1.fq,WT1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,WT1_R1.fq.gz WT1_R2.fq.gz,fastq fastq,6815123400.0,22717078.0,WT1 R1.fq.gz,0:150 1:150,A:1758536338;C:1650339290;G:1657619698;T:1748603714;N:24360,150,150,,,1758536338,1650339290,1657619698,1748603714,24360,SRX26734627,SRS23224776,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34140,SRR31360764,SRX26734626,SRS23224775,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu3,,strain:AB|isolate:mu3|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu3.fq,mu3.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu3_R1.fq.gz mu3_R2.fq.gz,fastq fastq,7304650200.0,24348834.0,mu3 R1.fq.gz,0:150 1:150,A:1934717193;C:1720864609;G:1730177787;T:1918863192;N:27419,150,150,,,1934717193,1720864609,1730177787,1918863192,27419,SRX26734626,SRS23224775,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34141,SRR31360765,SRX26734625,SRS23224774,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu2,,strain:AB|isolate:mu2|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu2.fq,mu2.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu2_R1.fq.gz mu2_R2.fq.gz,fastq fastq,7168114200.0,23893714.0,mu2 R1.fq.gz,0:150 1:150,A:1896004564;C:1692025000;G:1701080897;T:1878977280;N:26459,150,150,,,1896004564,1692025000,1701080897,1878977280,26459,SRX26734625,SRS23224774,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34142,SRR31360766,SRX26734624,SRS23224773,SRP545397,PRJNA1186411,Zebrafish intestine sequencing,PRJNA1186411,Other,To analyze transcriptomic changes of genes in the zebrafish intestine under specific conditions,,,,,mu1,,strain:AB|isolate:mu1|age:larvae|collection date:2019 04|geo loc name:China:Chongqing|sex:pooled male and female|tissue:intestine|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Danio Rerio: larvae intestine,mu1.fq,mu1.fq,nomal RAN Seq of zebrafish,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP545397,,,mu1_R1.fq.gz mu1_R2.fq.gz,fastq fastq,7262664600.0,24208882.0,mu1 R1.fq.gz,0:150 1:150,A:1922666653;C:1711620445;G:1720530432;T:1907824480;N:22590,150,150,,,1922666653,1711620445,1720530432,1907824480,22590,SRX26734624,SRS23224773,SRA2015506,Fudan University|School of Life Sciences,Fudan University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-11-15,Larval,Larval,Gut,Digestive System
34491,SRR31852177,SRX27211969,SRS23661292,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish BG rep3,GSM8703891,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish BG rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703891,GSM8703891: Zebrafish BG rep3; Danio rerio; RNA Seq,GSM8703891 r1,GSM8703891,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_3_R1.fastq.gz BG_3_R2.fastq.gz,fastq fastq,6899655382.0,22846541.0,GSM8703891 r1,0:151 1:151,A:1811966008;C:1615713130;G:1645022233;T:1826840592;N:113419,151,151,,,1811966008,1615713130,1645022233,1826840592,113419,SRX27211969,SRS23661292,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34492,SRR31852178,SRX27211968,SRS23661291,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish BG rep2,GSM8703890,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish BG rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703890,GSM8703890: Zebrafish BG rep2; Danio rerio; RNA Seq,GSM8703890 r1,GSM8703890,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_2_R1.fastq.gz BG_2_R2.fastq.gz,fastq fastq,6320533538.0,20928919.0,GSM8703890 r1,0:151 1:151,A:1636247942;C:1501072316;G:1530315619;T:1652793962;N:103699,151,151,,,1636247942,1501072316,1530315619,1652793962,103699,SRX27211968,SRS23661291,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34493,SRR31852179,SRX27211967,SRS23661290,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish BG rep1,GSM8703889,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish BG rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:Beta Glucan training and E. piscicida infection|time:Day 7,GSM8703889,GSM8703889: Zebrafish BG rep1; Danio rerio; RNA Seq,GSM8703889 r1,GSM8703889,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,BG_1_R1.fastq.gz BG_1_R2.fastq.gz,fastq fastq,6720003132.0,22251666.0,GSM8703889 r1,0:151 1:151,A:1771169227;C:1572565291;G:1597071360;T:1779087569;N:109685,151,151,,,1771169227,1572565291,1597071360,1779087569,109685,SRX27211967,SRS23661290,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34494,SRR31852180,SRX27211966,SRS23661289,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish EIB202 rep3,GSM8703888,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish EIB202 rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703888,GSM8703888: Zebrafish EIB202 rep3; Danio rerio; RNA Seq,GSM8703888 r1,GSM8703888,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_3_R1.fastq.gz EIB202_3_R2.fastq.gz,fastq fastq,6653244824.0,22030612.0,GSM8703888 r1,0:151 1:151,A:1715767195;C:1587994105;G:1617241387;T:1732132934;N:109203,151,151,,,1715767195,1587994105,1617241387,1732132934,109203,SRX27211966,SRS23661289,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34495,SRR31852181,SRX27211965,SRS23661288,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish EIB202 rep2,GSM8703887,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish EIB202 rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703887,GSM8703887: Zebrafish EIB202 rep2; Danio rerio; RNA Seq,GSM8703887 r1,GSM8703887,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_2_R1.fastq.gz EIB202_2_R2.fastq.gz,fastq fastq,7203983198.0,23854249.0,GSM8703887 r1,0:151 1:151,A:1847641462;C:1731806146;G:1763208826;T:1861209998;N:116766,151,151,,,1847641462,1731806146,1763208826,1861209998,116766,SRX27211965,SRS23661288,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34496,SRR31852182,SRX27211964,SRS23661287,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish EIB202 rep1,GSM8703886,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish EIB202 rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:E. piscicida infection|time:Day 7,GSM8703886,GSM8703886: Zebrafish EIB202 rep1; Danio rerio; RNA Seq,GSM8703886 r1,GSM8703886,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,EIB202_1_R1.fastq.gz EIB202_1_R2.fastq.gz,fastq fastq,6634863292.0,21969746.0,GSM8703886 r1,0:151 1:151,A:1708949626;C:1589664250;G:1615939413;T:1720201415;N:108588,151,151,,,1708949626,1589664250,1615939413,1720201415,108588,SRX27211964,SRS23661287,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34497,SRR31852183,SRX27211963,SRS23661286,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish mock rep3,GSM8703885,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish mock rep3,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703885,GSM8703885: Zebrafish mock rep3; Danio rerio; RNA Seq,GSM8703885 r1,GSM8703885,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_3_R1.fastq.gz Mock_3_R2.fastq.gz,fastq fastq,6938479596.0,22975098.0,GSM8703885 r1,0:151 1:151,A:1771058080;C:1670207033;G:1705035413;T:1792066207;N:112863,151,151,,,1771058080,1670207033,1705035413,1792066207,112863,SRX27211963,SRS23661286,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34498,SRR31852184,SRX27211962,SRS23661285,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish mock rep2,GSM8703884,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish mock rep2,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703884,GSM8703884: Zebrafish mock rep2; Danio rerio; RNA Seq,GSM8703884 r1,GSM8703884,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_2_R1.fastq.gz Mock_2_R2.fastq.gz,fastq fastq,7374531658.0,24418979.0,GSM8703884 r1,0:151 1:151,A:1885070518;C:1779385428;G:1810157081;T:1899798486;N:120145,151,151,,,1885070518,1779385428,1810157081,1899798486,120145,SRX27211962,SRS23661285,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34499,SRR31852185,SRX27211961,SRS23661284,SRP554424,PRJNA1204310,Trained immunity amplifies intestinal complement 3 to maintain Th17 cells against bacterial infection induced enteritis in zebrafish,GSE285528,Transcriptome Analysis,Infectious enteritis is often accompanied with immuno disorder of intestinal immune cells caused by microbials infection. Trained immunity is classically characterized by long term functional reprogramming of innate immune cells to combat infectious diseases. However whether the induction of trained immunity plays a role in protecting infectious enteritis remains largely unknown. Here through establishing an in vivo ß glucan training and E. piscicida infection model in zebrafish we observe that induction of trained immunity could alleviate bacterial infection caused enteritis. Moreover we identify intestinal complement C3 as a crucial target of trained immunity and could be amplified in response to bacterial infection. Furthermore we reveal that trained immunity could reverse the reduction of intestinal Th17 cells in C3 dependent manner to alleviate infectious enteritis. Taken together our results uncover the role of complement C3 mediated trained immunity in maintaining Th17 cells and intestine homeostasis and provide a theoretical strategy for immunotherapies of infectious enteritis. Overall design: RNA seq profiling of wildtype zebrafish in mock and PBS or ß glucan trained at Day 7 post secondary E. piscicida infection,,,,Zebrafish mock rep1,GSM8703883,,source name:Intestine|tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7|geo loc name:missing|collection date:missing,Zebrafish mock rep1,Constructing an index of the reference genome using HISAT2 v2.1.0 Assembly: GRCz21 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: csv files include FPKM values for each Sample,Intestine,10 µL yeast derived β glucan 10 mg/mL was intraperitoneally injected i.p. and post resting for 5 days 5 µL E. piscicida2 × 106 CFU/mL was challenged with through rectal injection,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,Three to six mpf AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle 14 h light/10 h dark.,tissue:Intestine|strain:AB|genotype:WT|treatment:no|time:Day 7,GSM8703883,GSM8703883: Zebrafish mock rep1; Danio rerio; RNA Seq,GSM8703883 r1,GSM8703883,1,The RNA of each individual sample was isolated by Trizol Invitrogen and chloroform. RNA libraries for RNA seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP554424,,,Mock_1_R1.fastq.gz Mock_1_R2.fastq.gz,fastq fastq,6563252448.0,21732624.0,GSM8703883 r1,0:151 1:151,A:1759569033;C:1514211809;G:1536003223;T:1753362072;N:106311,151,151,,,1759569033,1514211809,1536003223,1753362072,106311,SRX27211961,SRS23661284,SRA2042566,"Ahua lab, East China University of Science and Technology","Ahua lab, East China University of Science and Technology",,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2024-12-30,Adult,Adult,Gut,Digestive System
34517,SRR32044795,SRX27393953,SRS23824014,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr+VC 3,I,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 3,Cr+VC 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz,fastq fastq,6773536558.0,22428929.0,Cr+VC 3.R1.raw.fastq.gz,0:151 1:151,A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278,151,151,,,1792253952,1581454013,1629330621,1770470694,27278,SRX27393953,SRS23824014,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34518,SRR32044796,SRX27393952,SRS23824013,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr+VC 2,H,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 2,Cr+VC 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz,fastq fastq,7449518862.0,24667281.0,Cr+VC 2.R1.raw.fastq.gz,0:151 1:151,A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119,151,151,,,1969693675,1748150730,1771267240,1960378098,29119,SRX27393952,SRS23824013,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34519,SRR32044797,SRX27393951,SRS23824012,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr+VC 1,G,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 1,Cr+VC 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options: doNotUseSharq,Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq,fastq fastq,6865491179.0,45466829.0,Cr+VC 1.R1.raw.fastq.gz,0:151,A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474,151,,,,1830069736,1600281531,1626303427,1808809011,27474,SRX27393951,SRS23824012,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34520,SRR32044798,SRX27393950,SRS23824011,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr 3,F,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 3,Cr 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz,fastq fastq,6069804078.0,20098689.0,Cr 3.R1.raw.fastq.gz,0:151 1:151,A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079,151,151,,,1603886661,1431213970,1440806224,1593873144,24079,SRX27393950,SRS23824011,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34521,SRR32044799,SRX27393949,SRS23824010,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr 2,E,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 2,Cr 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options: doNotUseSharq,Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq,fastq fastq,8327156985.0,55146735.0,Cr 2.R1.raw.fastq.gz,0:151,A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145,151,,,,2181317777,1974793526,2003240106,2167771431,34145,SRX27393949,SRS23824010,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34522,SRR32044800,SRX27393948,SRS23824009,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Cr 1,D,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 1,Cr 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz,fastq fastq,7322067614.0,24245257.0,Cr 1.R1.raw.fastq.gz,0:151 1:151,A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557,151,151,,,1927213281,1727973559,1748866497,1917985720,28557,SRX27393948,SRS23824009,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34523,SRR32044801,SRX27393947,SRS23824008,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Con 3,C,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 3,Con 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz,fastq fastq,10329187314.0,34202607.0,Con 3.R1.raw.fastq.gz,0:151 1:151,A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354,151,151,,,2805764955,2343400161,2421657823,2758323021,41354,SRX27393947,SRS23824008,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34524,SRR32044802,SRX27393946,SRS23824007,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Con 2,B,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 2,Con 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz,fastq fastq,10789961398.0,35728349.0,Con 2.R1.raw.fastq.gz,0:151 1:151,A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353,151,151,,,2983305704,2396592872,2488165589,2921853880,43353,SRX27393946,SRS23824007,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34525,SRR32044803,SRX27393945,SRS23824006,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.,,,,Con 1,A,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 1,Con 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz,fastq fastq,7118179260.0,23570130.0,Con 1.R1.raw.fastq.gz,0:151 1:151,A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275,151,151,,,1874284939,1673861890,1718740497,1851263659,28275,SRX27393945,SRS23824006,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
38059,SRR1524245,SRX661010,SRS665985,SRP044781,PRJNA255848,Danio rerio Transcriptome,PRJNA255848,Transcriptome Analysis,Transcriptome analysis of 12 zebrafish tissues,parent bioproject:PRJNA255979,pubmed:27189481,Zebrafish intestine,Zebrafish intestine,F Dr 9,,strain:AB|age:5 month|biomaterial provider:INRA|sex:female|tissue:Intestine|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish intestine,F Dr 9,F Dr 9,Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,2000Application ReadForward11Application ReadReverse101,SRP044781,,,F_Dr_9_GCCAAT_L005_R2.fastq.gz F_Dr_9_GCCAAT_L005_R1.fastq.gz,fastq fastq,8637468200.0,43187341.0,F Dr 9 files,0:100 1:100,A:2270309093;C:2039596980;G:2056249938;T:2263331787;N:7980402,100,100,,,2270309093,2039596980,2056249938,2263331787,7980402,SRX661010,SRS665985,SRA176464,INRA|Fish Physiology and Genomics,INRA PhyloFish,2,0.94661,0.94511,0.06033,0.06049,0.75743,0.75747,0.43604,0.43901,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,France,2015-07-24,Adult,Adult,Gut,Digestive System
38269,SRR1609746,SRX730399,SRS719620,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine10,GSM1523041,,source name:intestine|tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,intestine10,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523041,GSM1523041: intestine10; Danio rerio; RNA Seq,GSM1523041,,1,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523041,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine10_2.fq.gz intestine10_1.fq.gz,fastq fastq,3638953000.0,18194765.0,GSM1523041 r1,0:100 1:100,A:944286084;C:877180113;G:870958371;T:946463708;N:64724,100,100,,,944286084,877180113,870958371,946463708,64724,SRX730399,SRS719620,SRA189240,GEO,Shanghai Ocean University,2,0.95871,0.95555,0.03654,0.03737,0.77546,0.77597,0.49972,0.50867,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38270,SRR1609745,SRX730398,SRS719619,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine18,GSM1523040,,source name:intestine|tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,intestine18,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523040,GSM1523040: intestine18; Danio rerio; RNA Seq,GSM1523040,,1,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523040,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine18_1.fq.gz intestine18_2.fq.gz,fastq fastq,3870426800.0,19352134.0,GSM1523040 r1,0:100 1:100,A:1034436410;C:900862332;G:899347839;T:1035707094;N:73125,100,100,,,1034436410,900862332,899347839,1035707094,73125,SRX730398,SRS719619,SRA189240,GEO,Shanghai Ocean University,2,0.93279,0.92997,0.0455,0.04571,0.76152,0.76228,0.44545,0.44882,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
38271,SRR1609744,SRX730397,SRS719618,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,intestine28,GSM1523039,,source name:intestine|tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,intestine28,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,intestine,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:intestine|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523039,GSM1523039: intestine28; Danio rerio; RNA Seq,GSM1523039,,1,Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523039,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,intestine28_1.fq.gz intestine28_2.fq.gz,fastq fastq,3710350200.0,18551751.0,GSM1523039 r1,0:100 1:100,A:987499090;C:870092319;G:865419689;T:987267641;N:71461,100,100,,,987499090,870092319,865419689,987267641,71461,SRX730397,SRS719618,SRA189240,GEO,Shanghai Ocean University,2,0.94613,0.94058,0.04736,0.04784,0.7599,0.76288,0.51653,0.51797,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Gut,Digestive System
41072,SRR3655801,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS410.fastq.gz,fastq,1402184556.0,18692635.0,GSM2195935 r1,0:75.01 1:0,A:363262740;C:326626075;G:322630446;T:389582075;N:83220,75,0,,,363262740,326626075,322630446,389582075,83220,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92115,,0.08008,,0.7389,,0.52691,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41073,SRR3655802,SRX1836012,SRS1495476,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,GSM2195935,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195935,GSM2195935: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #3; Danio rerio; RNA Seq,GSM2195935,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195935,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS410.fastq.gz,fastq,3450884531.0,46005067.0,GSM2195935 r2,0:75.01 1:0,A:874448337;C:808236306;G:797225707;T:970673048;N:301133,75,0,,,874448337,808236306,797225707,970673048,301133,SRX1836012,SRS1495476,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93035,,0.08192,,0.73271,,0.52273,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41074,SRR3655799,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS409.fastq.gz,fastq,1422635421.0,18963577.0,GSM2195934 r1,0:75.02 1:0,A:362173330;C:332883466;G:329078937;T:398420070;N:79618,75,0,,,362173330,332883466,329078937,398420070,79618,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92474,,0.07466,,0.73423,,0.50871,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41075,SRR3655800,SRX1836011,SRS1495475,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,GSM2195934,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195934,GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq,GSM2195934,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195934,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS409.fastq.gz,fastq,3549432159.0,47315580.0,GSM2195934 r2,0:75.02 1:0,A:893492844;C:832741437;G:822208498;T:1000698758;N:290622,75,0,,,893492844,832741437,822208498,1000698758,290622,SRX1836011,SRS1495475,SRA432774,GEO,Children's Hospital Los Angeles,1,0.93197,,0.07554,,0.73109,,0.50825,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41076,SRR3655797,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r1,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92971,,0.10926,,0.73016,,0.51418,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41077,SRR3655798,SRX1836010,SRS1495474,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,GSM2195933,,tissue:full thickness intestine|status:SBS,Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SBS,GSM2195933,GSM2195933: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #1; Danio rerio; RNA Seq,GSM2195933,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195933,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS408.fastq.gz,fastq,1400640841.0,18670640.0,GSM2195933 r2,0:75.02 1:0,A:363544908;C:324586412;G:320620988;T:391797091;N:91442,75,0,,,363544908,324586412,320620988,391797091,91442,SRX1836010,SRS1495474,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92977,,0.10933,,0.73008,,0.51355,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Larval,Larval,Gut,Digestive System
41078,SRR3655795,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS383.fastq.gz,fastq,1510741670.0,20138480.0,GSM2195932 r1,0:75.02 1:0,A:374411447;C:361418430;G:359803924;T:415021333;N:86536,75,0,,,374411447,361418430,359803924,415021333,86536,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94789,,0.05269,,0.77753,,0.53939,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41079,SRR3655796,SRX1836009,SRS1495472,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,GSM2195932,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #3,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195932,GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq,GSM2195932,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195932,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS383.fastq.gz,fastq,3623681121.0,48303841.0,GSM2195932 r2,0:75.02 1:0,A:881893112;C:869893713;G:867139931;T:1004485159;N:269206,75,0,,,881893112,869893713,867139931,1004485159,269206,SRX1836009,SRS1495472,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95546,,0.05225,,0.77218,,0.53519,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41080,SRR3655793,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS381.fastq.gz,fastq,1348860046.0,17985061.0,GSM2195931 r1,0:75.00 1:0,A:350940564;C:313266568;G:309387786;T:375159308;N:105820,75,0,,,350940564,313266568,309387786,375159308,105820,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.92348,,0.06356,,0.77252,,0.52707,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41081,SRR3655794,SRX1836008,SRS1495473,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,GSM2195931,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #2,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195931,GSM2195931: Proximal S1 intestine in zebrafish 2 wks post sham surgery #2; Danio rerio; RNA Seq,GSM2195931,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195931,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS381.fastq.gz,fastq,3298786881.0,43979655.0,GSM2195931 r2,0:75.01 1:0,A:829523096;C:775146066;G:763427556;T:930352935;N:337228,75,0,,,829523096,775146066,763427556,930352935,337228,SRX1836008,SRS1495473,SRA432774,GEO,Children's Hospital Los Angeles,1,0.9361,,0.06336,,0.76353,,0.54746,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41082,SRR3655791,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,02May15_KS380.fastq.gz,fastq,1448364484.0,19307379.0,GSM2195930 r1,0:75.02 1:0,A:359052072;C:343824905;G:344804667;T:400589883;N:92957,75,0,,,359052072,343824905,344804667,400589883,92957,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.94277,,0.05284,,0.77881,,0.57769,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41083,SRR3655792,SRX1836007,SRS1495471,SRP076398,PRJNA325275,Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption: RNA Sequencing a Zebrafish SBS Model,GSE83195,Transcriptome Analysis,Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects and tested this in a zebrafish SBS model. Methods: With IACUC approval adult male wild type zebrafish underwent SBS laparotomy proximal stoma distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks the proximal intestine was harvested RNA isolated and external RNA controls consortium ERCC controls spiked into each sample sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed. CyclinD1 CyclinB1 SAA1 IFN gamma and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling complement system coagulation cell proliferation cellular barrier production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis gluconeogenesis glycogenolysis fatty acid oxidation & activation and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher CyclinB1 2.8 fold higher SAA1 4.5 fold higher IFN gamma 2.1 fold higher and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish intestine were generated by deep sequencing in triplicate.,,pubmed:28118819,,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,GSM2195930,,tissue:full thickness intestine|status:SHAM,Proximal S1 intestine in zebrafish 2 wks post sham surgery #1,Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values counts DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser,full thickness intestine,,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,,status:SHAM,GSM2195930,GSM2195930: Proximal S1 intestine in zebrafish 2 wks post sham surgery #1; Danio rerio; RNA Seq,GSM2195930,,1,Full thickness section of intestine was removed and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations,GEO Accession:GSM2195930,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP076398,,,27May15_KS380.fastq.gz,fastq,3599154025.0,47976708.0,GSM2195930 r2,0:75.02 1:0,A:875615940;C:857379635;G:859609503;T:1006260031;N:288916,75,0,,,875615940,857379635,859609503,1006260031,288916,SRX1836007,SRS1495471,SRA432774,GEO,Children's Hospital Los Angeles,1,0.95037,,0.0525,,0.77147,,0.5711,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-06-09,Undetermined,Undetermined,Gut,Digestive System
41575,SRR5045902,SRX2368488,SRS1814332,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 2,GSM2401374,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401374,GSM2401374: MutCV 2; Danio rerio; RNA Seq,GSM2401374,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401374,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_2.fastq,fastq,3876906576.0,76017776.0,GSM2401374 r1,0:51 1:0,A:957781980;C:915286453;G:859927041;T:1143804372;N:106730,51,0,,,957781980,915286453,859927041,1143804372,106730,SRX2368488,SRS1814332,SRA497672,GEO,Duke University School of Medicine,1,0.96196,,0.11375,,0.70887,,0.53406,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41576,SRR5045901,SRX2368487,SRS1814330,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutCV 1,GSM2401373,,source name:zebrafish digestive tracts|condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401373,GSM2401373: MutCV 1; Danio rerio; RNA Seq,GSM2401373,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401373,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutCV_1.fastq,fastq,3835824444.0,75212244.0,GSM2401373 r1,0:51 1:0,A:946407906;C:904393791;G:851683286;T:1133241327;N:98134,51,0,,,946407906,904393791,851683286,1133241327,98134,SRX2368487,SRS1814330,SRA497672,GEO,Duke University School of Medicine,1,0.95795,,0.11761,,0.70481,,0.53357,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41577,SRR5045900,SRX2368486,SRS1814331,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 2,GSM2401372,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401372,GSM2401372: MutGF 2; Danio rerio; RNA Seq,GSM2401372,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401372,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_2.fastq,fastq,3299677866.0,64699566.0,GSM2401372 r1,0:51 1:0,A:809247440;C:784035543;G:731742820;T:974610541;N:41522,51,0,,,809247440,784035543,731742820,974610541,41522,SRX2368486,SRS1814331,SRA497672,GEO,Duke University School of Medicine,1,0.96247,,0.1049,,0.74034,,0.5525,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41578,SRR5045899,SRX2368485,SRS1814329,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,MutGF 1,GSM2401371,,source name:zebrafish digestive tracts|condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,MutGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:Mutant hnf4a / |tissue:Larval digestive tract,GSM2401371,GSM2401371: MutGF 1; Danio rerio; RNA Seq,GSM2401371,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401371,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,MutGF_1.fastq,fastq,3734921199.0,73233749.0,GSM2401371 r1,0:51 1:0,A:923493830;C:879193170;G:840678282;T:1091454504;N:101413,51,0,,,923493830,879193170,840678282,1091454504,101413,SRX2368485,SRS1814329,SRA497672,GEO,Duke University School of Medicine,1,0.96328,,0.1099,,0.73492,,0.50455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41579,SRR5045898,SRX2368484,SRS1814328,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 3,GSM2401370,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401370,GSM2401370: WTCV 3; Danio rerio; RNA Seq,GSM2401370,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401370,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_3.fastq,fastq,3928418412.0,77027812.0,GSM2401370 r1,0:51 1:0,A:966197912;C:939595492;G:912123411;T:1110393846;N:107751,51,0,,,966197912,939595492,912123411,1110393846,107751,SRX2368484,SRS1814328,SRA497672,GEO,Duke University School of Medicine,1,0.97188,,0.08862,,0.7357,,0.53339,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41580,SRR5045897,SRX2368483,SRS1814327,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 2,GSM2401369,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401369,GSM2401369: WTCV 2; Danio rerio; RNA Seq,GSM2401369,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401369,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_2.fastq,fastq,3782941473.0,74175323.0,GSM2401369 r1,0:51 1:0,A:928563733;C:910471684;G:872137892;T:1071716851;N:51313,51,0,,,928563733,910471684,872137892,1071716851,51313,SRX2368483,SRS1814327,SRA497672,GEO,Duke University School of Medicine,1,0.97097,,0.09668,,0.74255,,0.55455,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41581,SRR5045896,SRX2368482,SRS1814326,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTCV 1,GSM2401368,,source name:zebrafish digestive tracts|condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTCV 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:CV|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401368,GSM2401368: WTCV 1; Danio rerio; RNA Seq,GSM2401368,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401368,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTCV_1.fastq,fastq,3643146954.0,71434254.0,GSM2401368 r1,0:51 1:0,A:877377891;C:875020597;G:839793450;T:1050862579;N:92437,51,0,,,877377891,875020597,839793450,1050862579,92437,SRX2368482,SRS1814326,SRA497672,GEO,Duke University School of Medicine,1,0.9683,,0.08514,,0.73525,,0.55486,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41582,SRR5045895,SRX2368481,SRS1814325,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 3,GSM2401367,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 3,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401367,GSM2401367: WTGF 3; Danio rerio; RNA Seq,GSM2401367,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401367,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_3.fastq,fastq,3462802386.0,67898086.0,GSM2401367 r1,0:51 1:0,A:843407439;C:830117704;G:803633976;T:985548502;N:94765,51,0,,,843407439,830117704,803633976,985548502,94765,SRX2368481,SRS1814325,SRA497672,GEO,Duke University School of Medicine,1,0.97202,,0.08623,,0.75939,,0.56558,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41583,SRR5045894,SRX2368480,SRS1814324,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 2,GSM2401366,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 2,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401366,GSM2401366: WTGF 2; Danio rerio; RNA Seq,GSM2401366,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401366,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_2.fastq,fastq,3699149799.0,72532349.0,GSM2401366 r1,0:51 1:0,A:907425678;C:884609705;G:855651232;T:1051368070;N:95114,51,0,,,907425678,884609705,855651232,1051368070,95114,SRX2368480,SRS1814324,SRA497672,GEO,Duke University School of Medicine,1,0.96861,,0.08856,,0.75223,,0.55327,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System
41584,SRR5045893,SRX2368479,SRS1814323,SRP093775,PRJNA354631,Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha zebrafish RNA seq,GSE90446,Transcriptome Analysis,We performed RNA seq from 6 dpf hnf4a / and hnf4a+/+ zebrafish larval digestive tracts raised in the absence Germ Free GF or presence Conventionalized CV of microbiota. We found that zebrafish hnf4a activates almost half of the microbiota suppressed genes indicating that the microbiota supress Hnf4a trans activity. We also provide evidence suggesting that microbial suppression of Hnf4a may contribute to IBD pathogenesis. Overall design: Generation and analysis of RNA seq from hnf4a / and hnf4a+/+ zebrafish larvae in the absence Germ Free GF or presence Conventionalized CV microbiota.,parent bioproject:PRJNA354702,pubmed:28385711,,WTGF 1,GSM2401365,,source name:zebrafish digestive tracts|condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,WTGF 1,Zebrafish RNA seq reads were aligned to the zebrafish genome danRer7 using TopHat2 v0.6 on a private Galaxy server using de novo splice junction mapping default TopHat settings bam files were normalized by sequencing depth to generate bigWigs Genome build: DanRer7 zv9 Supplementary files format and content: bigWig,zebrafish digestive tracts,Lines were maintained on a TL/Tü background using established protocols approved by the Animal Studies Committee at the University of North Carolina at Chapel Hill and Duke University School of Medicine. Conventionally raised zebrafish were reared and maintained as described Westerfield 2000. Production colonization maintenance and sterility testing of gnotobiotic zebrafish were performed as described Pham et al. 2008.,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,,condition:GF|genotype:WT hnf4a+/+|tissue:Larval digestive tract,GSM2401365,GSM2401365: WTGF 1; Danio rerio; RNA Seq,GSM2401365,,1,Zebrafish digestive tracts n = 13 – 20 per condition per genotype were removed by microdissection and resuspended in 1 mL TRIzol Ambion/Invitrogen/ThermoFisher Scientific 15596026. Larval digestive tracts were lysed by being passing through a 25 G needle followed by a 27.5 G needle 5 times each. 200 uL of chloroform was added to the TRIzol and the sample was vortexed on high for 30 seconds at room temperature. The samples were incubated at room temperature for 2 minutes and centrifuged at 12 000 x g for 15 minutes at 4°C. The top aqueous layer was removed and added to equal volume of isopropanol. The nucleic acids were isolated using a column based RNA isolation kit Ambion Cat 12183018A with an on column DNase I RNase free treatment New England Biolabs M0303L to remove DNA contamination. RNA was eluted off the column in nuclease free water quantified using a Qubit 2.0 and stored at 80°C until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 with 4 samples per lane in the flow cell.,GEO Accession:GSM2401365,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP093775,,,WTGF_1.fastq,fastq,3948593247.0,77423397.0,GSM2401365 r1,0:51 1:0,A:951060123;C:949871425;G:909862458;T:1137745436;N:53805,51,0,,,951060123,949871425,909862458,1137745436,53805,SRX2368479,SRS1814323,SRA497672,GEO,Duke University School of Medicine,1,0.97252,,0.08483,,0.74418,,0.54605,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2016-11-22,Larval,Larval,Gut,Digestive System